Results (PhD Chapter 2)


This series of files compile all analyses done during Chapter 2:

All analyses have been done with R 3.6.0.

Click on the table of contents in the left margin to assess a specific analysis
Click on a figure to zoom it

To assess Section 2, click here.
To go back to the summary page, click here.


Human activities considered for the analyses:

Data is also available for the number of captured individuals for dogwhelk (Buccinum sp.), common crab (Cancer irroratus), snowcrab (Chinoecetes opilio), nordic shrimp (Pandalus borealis), arctic surfclam (Mactromeris polynyma) and american lobster (Homarus americanus) fisheries.


Workspace preparation

Here, we use data from subtidal ecosystems (see metadata files for more information)
Only stations that have been sampled both for abiotic parameters and benthic species were included.
The script below includes personnal functions, refined data, parameters for each campaign and global means, sd, se.


1. Maps

Depth

Isobaths

2. Modelling of human activities influence (WIP)

The influence of each human activity has been modelled at each station, in order to be later used in HMSC models.

We calculated a probability of influence for each activity \(P_{ij}\). For non-fisheries activities, the index \(I_{ij}\) has been calculated based on the distance from the source(s), bathymetry and hydrodynamics influences. We also included a weighting parameter specific for each activity, .

\[ P_{ij} = w_{j} . I_{ij} \]

\[ I_{ij} = \left( 1 - \frac{D_{ij}}{D_{max, j}} \right) . f_{j} \left( 1 - \frac{D_{ij}}{D_{max, j}} \right) . \Delta Z_{i} . H_{i} \]

  • \(i\) is a station
  • \(j\) is a human activity
  • \(f_{j}\) is the decay function of activity \(j\)
  • \(w_{j}\) is the weighting parameter for activity \(j\)
  • \(D_{ij}\) is the distance of station \(i\) from the source of activity \(j\)
  • \(\Delta Z_{i}\) is the bathymetry index at station \(i\)
  • \(H_{i}\) is the hydrodynamic index at station \(i\)

i) Distance form the source

This corresponds to \(D_{ij}\) in Formula 2.

First, we need to calculate the distance of each station from the source(s) of the activity. This proxy will allow to take coasts and island into consideration (necessary at BSI), and will then be used to calculated the probabilities of influence.

Here are the minimum distances of each station from the source of each activity (in meters, calculated with gdistance):

station_id city dredging industry mooring sewers_rain sewers_waste wharves_city wharves_industry
1 8090 1141 361 1012 2099 1321 8334 275
2 7364 742 186 1445 1085 186 7339 165
3 8053 1085 171 1156 1910 1131 8240 86
4 8246 1354 542 949 2356 1578 8548 532
5 8215 1415 763 742 2565 1786 8622 741
6 6273 1568 330 2282 491 1473 6202 428
7 6154 1592 433 2267 609 1540 6083 546
8 6961 1177 495 2044 516 722 6890 119
9 6984 1073 447 1941 577 618 6913 238
10 7809 949 0 1383 1377 599 7861 119
11 542 4253 2138 1880 3744 4211 618 2899
12 424 4111 1996 1984 3832 4299 447 2757
13 594 4324 2209 1828 3723 4190 703 2970
14 661 4276 2162 1761 3805 4272 684 2922
15 532 4015 1900 1850 3966 4433 447 2661
16 1850 447 165 4247 5300 7968 1850 665
17 1627 722 82 3972 5105 7745 1627 424
18 1523 893 186 3800 4963 7642 1523 351
19 NA NA NA NA NA NA NA NA
20 0 2253 119 2813 5007 6118 0 899
21 NA NA NA NA NA NA NA NA
22 NA NA NA NA NA NA NA NA
23 NA NA NA NA NA NA NA NA
24 NA NA NA NA NA NA NA NA
25 NA NA NA NA NA NA NA NA
26 11612 10102 10643 11620 8952 12003 11612 10851
27 11746 10236 10777 11754 9086 12137 11746 10985
28 NA NA NA NA NA NA NA NA
29 NA NA NA NA NA NA NA NA
30 11509 9998 10539 11517 8848 11899 11509 10747
31 7883 4608 5808 9963 10412 13492 7883 6699
32 7883 4608 5808 9963 10412 13492 7883 6699
33 NA NA NA NA NA NA NA NA
34 7764 4490 5689 9858 10346 13425 7764 6580
35 7741 4466 5685 9821 10241 13321 7741 6557
36 NA NA NA NA NA NA NA NA
37 NA NA NA NA NA NA NA NA
38 NA NA NA NA NA NA NA NA
39 NA NA NA NA NA NA NA NA
40 NA NA NA NA NA NA NA NA
101 6510 1255 516 2081 516 1112 6439 330
102 5652 4066 5425 0 6524 5737 7233 5405
103 8719 2395 1692 1131 3828 3049 9251 2018
104 7478 5097 6132 1625 7529 6630 9171 6111
105 2005 4831 5105 1631 3878 3989 3686 5866
106 2091 7553 6835 4089 3193 2842 5223 7615
107 2310 5963 6509 2498 4057 3932 4916 7270
108 454 5579 3469 2127 2835 3302 1876 4230
109 1115 4916 2830 1363 3701 4168 1454 3562
110 2312 960 1073 3894 4512 7630 2312 1258
111 8076 5300 3013 10546 11711 14194 8076 6906
112 2444 0 728 4769 5633 8562 2444 1260
113 4732 2043 914 7202 8368 10851 4732 3563
114 4192 2018 3033 165 2560 3254 4252 3034
115 3590 3198 4704 0 4997 4828 4743 4704
116 4704 1836 3341 0 4086 3466 5539 3341
117 3217 2301 2401 3900 3412 6529 3238 2539
118 8836 7570 6297 7275 4606 7657 8830 6620
119 9656 8616 7810 8788 6119 9170 9677 8133
120 7481 4206 5560 9561 9776 12856 7481 6297
121 7855 4769 6139 9722 8597 11677 7855 6651
122 6981 3706 5003 9061 9632 12712 6981 5797
123 11240 9563 10211 11248 8580 11631 11240 10396
124 10042 6768 7535 12281 12956 16036 10042 8858
125 6926 330 516 1152 1363 598 6958 495
126 8624 1828 537 1073 2851 2072 9049 1027
127 6559 1627 165 2453 186 1359 6488 171
128 6224 950 991 1606 1011 1225 6152 825
129 5985 855 1260 1259 1423 1449 5914 1237
130 7269 990 119 1791 676 275 7198 186
131 6956 495 351 1363 1156 491 6911 351
132 6606 0 825 862 1672 949 6696 825
134 7185 330 516 970 1575 676 7313 537
135 6783 0 1011 491 1977 1156 7054 1032
136 7986 1018 190 1073 1928 1150 8192 119
137 7651 760 537 676 2138 1259 7981 516
138 7368 770 970 247 2448 1568 7813 949
139 8624 1828 537 1073 2851 2072 9049 1027
140 8366 1720 949 676 2945 2166 8811 1121
141 8079 1625 1444 361 3159 2279 8524 1378
142 7551 2398 3062 808 4598 3699 8617 3010
143 7338 2185 2906 551 4443 3544 8361 2870
144 7148 2090 2932 361 4406 3507 8171 2911
145 7493 2613 3315 855 4851 3952 8646 3263
146 7266 2399 3159 599 4695 3797 8390 3138
147 7124 2257 3118 428 4592 3693 8219 3097
148 6270 1539 2867 0 3985 3179 7192 2846
149 5702 1072 2578 0 3510 2723 6393 2599
150 5363 763 2269 0 3013 2393 5784 2269
151 5368 1650 3155 0 4088 3301 6261 3176
152 5014 1402 2908 0 3694 3032 5719 2908
153 4717 1301 2807 0 3301 2931 5176 2807
154 4419 2125 3631 0 4291 3755 5311 3631
155 4254 1899 3405 0 3842 3529 4959 3405
156 4220 1798 3118 0 3196 3242 4540 3118
157 722 4110 1995 1679 3991 4458 637 2756
158 926 3990 1947 1378 4300 4767 855 2636
159 1586 3724 1957 960 3583 5736 1501 2452
160 309 3279 1164 2089 4664 5131 190 1925
161 832 2878 1102 1815 4101 5945 780 1596
162 1188 2859 1354 1824 3714 6293 1167 1663
163 247 2233 309 2585 4702 6216 268 879
164 970 2242 903 2442 4087 6596 991 1083
165 1342 2337 1255 2346 3754 6554 1363 1330
166 981 1330 186 3364 4917 7099 981 186
167 1177 1359 454 3335 4703 7249 1177 380
168 2290 1406 1338 3587 4066 7183 2290 1445
169 1389 931 86 3763 5058 7508 1389 186
170 2085 855 805 3866 4654 7772 2085 990
171 2435 1169 1280 3848 4304 7421 2435 1465
172 7469 4194 5394 9708 10383 13501 7469 6285
173 7479 4204 5404 9631 10231 13311 7479 6295
174 7312 4038 5237 9507 10183 13263 7312 6128
175 6410 3136 4393 8577 9252 12370 6410 5226
176 7576 4302 5694 9656 9738 12818 7576 6392
177 6910 3635 4951 8990 9547 12626 6910 5726
178 6412 3157 4625 8492 8948 12028 6412 5228
179 7459 4242 5679 9538 9444 12524 7459 6274
180 6864 3647 5100 8944 9110 12190 6864 5680
181 7837 4659 6122 9801 9302 12381 7837 6634
182 7496 4317 5780 9421 8922 12002 7496 6292
183 7273 4095 5558 9160 8684 11764 7273 6070
184 8120 4942 6405 9988 9310 12390 8120 6917
185 7928 4750 6213 9796 8901 11981 7928 6725
186 7669 4583 5953 9537 8474 11553 7669 6465
187 9656 8616 7810 8788 6119 9170 9677 8133
188 8840 7574 6301 7279 4610 7661 8834 6625
189 6556 5368 4095 5073 2404 5455 6608 4418
190 4464 3070 2066 2349 454 3383 4443 2346
191 3263 2969 3860 0 3053 4205 3301 3861
192 926 3348 1406 1549 4296 5367 832 2052
193 5407 5138 6498 558 7154 6810 7478 6477
194 2044 7471 6768 4022 3174 2861 5156 7548
195 1834 4873 4963 1673 3735 3885 3515 5724
196 723 4894 2779 1755 3350 3817 1273 3540
197 1070 4536 2450 1383 3866 4333 1150 3182
198 2861 5673 6840 2163 4608 4483 5247 7179
199 4773 3485 4949 0 5944 5157 6131 4949
200 4281 4019 2784 3056 1027 4144 4259 3107
201 5678 4859 3586 4522 1895 4946 5699 3909
202 9838 8161 8808 9932 7410 10461 9838 8993
203 8160 5446 6646 9330 7771 10851 8160 7018
204 6693 4042 5179 7832 6316 9396 6693 5552
205 3754 1155 2208 5621 6297 9414 3754 2581
206 2950 165 1234 5053 5729 8846 2950 1746
207 3891 703 2014 6318 6993 10010 3891 2707
208 5126 1881 3077 7495 8171 11245 5126 3942
209 5216 3635 2362 3340 671 3722 5195 2685
211 7071 4295 2779 9541 10707 13190 7071 5901
212 7174 4030 4123 9644 10320 13293 7174 6004
214 8259 5133 4563 10728 11480 14377 8259 7089
215 599 6124 4397 2839 2310 2556 2804 5177
216 1033 5664 4609 2457 2809 3017 3017 5370
217 1540 5183 4893 2029 3379 3529 3315 5654
218 361 6079 4041 2721 2328 2602 2448 4821
219 893 5365 4181 2081 3041 3315 2588 4942
220 1530 4869 4583 1673 3565 3812 3135 5344
221 4799 2066 1033 7269 8435 10917 4799 3629
222 4790 2014 1420 7260 8426 10909 4790 3621
223 4820 2043 1673 7289 8455 10938 4820 3650
224 5626 2849 1307 8095 9261 11744 5626 4456
225 5617 2841 1694 8087 9252 11735 5617 4447
226 5523 2746 2020 7992 9158 11641 5523 4353
228 8431 2832 2721 1454 4656 3777 9367 2876
229 6087 4186 5057 6688 5110 8190 6087 5242
230 2785 1640 1755 3873 3953 7070 2785 1940
231 7144 4503 5615 1198 6934 6035 8649 5594
232 NA NA NA NA NA NA NA NA
233 NA NA NA NA NA NA NA NA
234 NA NA NA NA NA NA NA NA
235 11323 9646 10293 11331 8662 11713 11323 10478
236 3676 3177 4683 0 5018 4807 4828 4683
237 8365 5651 6850 9041 7222 10273 8365 7223
238 4640 3517 3694 5195 3838 6918 4640 3879
239 4625 2640 4187 0 5015 4228 5778 4166
240 5575 2352 3712 0 4811 4024 6728 3733
241 3209 2809 4191 0 4025 4315 3972 4191

The values of \(D_{ij}\) are presented on the following maps.

CityInf

InduInf

DredSit

MoorSit

RainSew

WastSew

CityWha

InduWha

ii) Decay function

This corresponds to \(f_{j}\) in Formula 2.

To be added.

iii) Bathymetry index

This corresponds to \(\Delta Z_{i}\) in Formula 2.

To be added.

iv) Hydrodynamic index

This corresponds to \(H_{i}\) in Formula 2.

To be added.

v) Index of influence

This corresponds to \(I_{ij}\) in Formula 2.

To be added.

vi) Weighting parameter

This corresponds to \(w_{j}\) in Formula 1.

The following table shows the weights \(w_{j}\) for each human activity:

activity weights
CityInf 1
InduInf 1
DredSit 1
MoorSit 1
RainSew 1
WastSew 1
CityWha 1
InduWha 1
FishTrap 1
FishTraw 1
FishLine 1
FishNet 1
FishDred 1

vii) Probability of influence

This corresponds to \(P_{ij}\) in Formula 1.

To be added.


Elliot Dreujou

2019-09-09